Inferences of African evolutionary history from genomic data

Abstract

Africa is the origin of anatomically modern humans and a continent of linguistic, cultural, environmental, phenotypic, and genetic diversity. However, African populations remain underrepresented in genetic studies, which have largely focused on individuals with European and Asian ancestry. The expansion of high-throughput 'omic' technologies to interrogate multiple tissue types across many biomolecules-DNA, proteins, epigenetic modifications, metabolites, and others-has heralded a new era of investigation into African history. In this review, we summarize how some of these recent advances have been applied to contemporary sub-Saharan African populations to inform studies on human origins and adaptation.

Figure 1

Map of Africa showing the distribution of the major language families, the location of hominid remains discussed in the text, and major migration routes of AMH through the continent within the past 10 ky. The Bantu expansion started around 5–4 kya from Cameroon/Nigeria border, initially from west to east, either north or south of the rainforest, to the Great Lakes of Uganda by around 3 kya and then from east to south in the last 2.5 ky, rapidly expanding into central and southern Africa, reaching Mozambique ~1.8 kya and South Africa ~1.5 kya. Another dispersion occurred ~3.5 kya from Cameroon, moving south to Angola. The spread of pastoralism into sub-Saharan Africa occurred around 4.5 kya (for a review see Pedro Soares et al. [36^•]. Agropastoralist, Afroasiatic populations migrated from Ethiopia into Kenya and Tanzania within the past 5 ky [42]. After admixing with Bantu groups, pastoralist populations from eastern Africa migrated through Tanzania to southern Africa around 2.4 kya [77]. Migrations through the Sahel occurred bidirectionally between east and west Africa in the past 8 ky [27,30]. There are many fossil sites of archaic and early AMH populations in Africa. A handful of sites important to discussions on human origins and archaic introgression are listed here. Herto: The well-preserved cranial remains of three individuals, dated to ~160 kya, were recovered at Herto Bouri, near the Middle Awash of Ethiopia. The crania are robust, consistent with other large archaic subspecies of Homo fossils found in Africa, but have endocranial morphology and facial features typical of modern Homo sapiens; thus they are thought to represent an extinct subspecies of Homo sapiens. Mota: The first ancient DNA analysis from Africa came from a ~4.5 ky old fossil found in the Mota Cave in the Ethiopian highlands. This fossil set the timing of reverse gene flow from Eurasia into Eastern Africa AMH ~1.5 ky earlier than prior estimates. Omo Kibish: Two crania, named Omo 1 and Omo 2, as well as post-cranial skeletal elements were found near the Omo River in Ethiopia. Dated to 195 kya, they possess a cranial vault height similar to AMH, situating them as early members of the Homo sapiens lineage. Of the two crania, Omo 1 has stronger morphological similarity to modern humans.